CIP - Lung segmentation labels error

[El Omeiri, Stephanie]

Hello, 

My name is Stephanie El Omeiri, I am a postdoc researcher at CHOP working on a project involving lung segmentation and volumetry. I am using the chest imaging platform extension to generate segmentation using the interactive segmentation tool in it, but as the segmentations are not always accurate, I have to use segment editor manually to fix them myself. I was not able to switch to segment editor and edit those maps unless I save the data and then upload the CT and the map (upload as segmentation).  I believe that when I am transforming the "partialLungLabelMap" into a segmentation, I am losing the labels of all the lobes. CIP labels each color with a name - red for RUL, blue for RML, etc. When I transform it into a segmentation, 3Dslicer changes the labels of the color to the default labels the software uses. For example, red is RUL for CIP, but for 3DSlicer is the Precentral gyrus. 

When I tried to run the parenchyma analysis on an edited segmentation it says "must contain segments right lung left lung other" because 3Dslicer replaced those color labels for the one the software uses by default. And then Parenchymal analysis doesn't recognize those new labels, and it will not run. 

I tried to rename the segmentation manually, but it crashed when I ran CIP with the new labels or gave me the error again.   Can you show me how I can I edit the segmentation map without error? What would be the easiest way? I would really appreciate your help; I can also meet virtually if further explanation is needed! I have attached a screenshot of the error. 

Thank you so much, 

Stephanie 

[El Omeiri, Stephanie]

Hi, 

Kind reminder of the email above! I really need some help with CIP !! 

Thank you, 

Stephanie 

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From: El Omeiri, Stephanie
Sent: Tuesday, September 3, 2024 12:56 PM
To: chestimagingp...@googlegroups.com <chestimagingp...@googlegroups.com>
Subject: CIP - Lung segmentation labels error